Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin

Abstract

Akkermansia muciniphila, a commensal bacterium commonly found in healthy gut microbiota, is widely considered a next-generation beneficial bacterium candidate to improve metabolic and inflammatory disorders. Recently the EFSA's Panel on Nutrition, Novel food, and Food Allergens has declared that pasteurized A. muciniphila DSM 22959^T (also Muc^T, ATCC BAA-835) can be considered safe as a novel food, opening the door to its commercialization as a food supplement. Despite its recognized health benefits, there is still little information regarding the antimicrobial susceptibility of this species and reference cut-off values to distinguish strains with intrinsic or acquired resistance from susceptible strains. In this study, we combined a genomic approach with the evaluation of the antibiotic susceptibility in five human A. muciniphila isolates. Genomic mining for antimicrobial resistance genes and MICs determinations revealed that only one strain harboring tetW gene showed resistance to tetracycline, whereas all A. muciniphila strains showed low sensitivity to ciprofloxacin and aminoglycosides with no genotypic correlation. Although all strains harbor the gene adeF, encoding for a subunit of the resistance-nodulation-cell division efflux pump system, potentially involved in ciprofloxacin resistance, the susceptibility towards ciprofloxacin determined in presence of efflux pump inhibitors was not affected. Overall, our outcomes revealed the importance to extend the antibiotic susceptibility test to a larger number of new isolates of A. muciniphila to better assess the safety aspects of this species.

Figure 1

Comparative genomics analysis of the 193 Akkermansia sp. genomes. (A) Pangenome content. (B) New genes content variation as new genomes are added to the analysis.

Figure 2

Phylogenetic tree of the 193 Akkermansia sp. genomes. The shell genes were used for the clusterization based on gene presence (dark blue) or absence (white). The genomes are clusterized into three groups corresponding to Akkermansia sp. SGB9228 (11 genomes), SGB9223(69 genomes), A. muciniphila (113 genomes). The yellow zone of the tree highlights the position of the newly isolated A. muciniphila strains characterized in this study.

Figure 3

(A) Accumulation of ethidium bromide in A. muciniphila strains in absence (white bars) and in presence (black bars) of CCCP after 60 min of incubation. (B) Kinetics of ethidium bromide accumulation by A. muciniphila strains in absence (solid lines) and in presence (dashed lines) of CCCP. Data are shown as the average values of three replicates, with standard deviation. RFU, Relative Fluorescence Unit.